Viral metagenomics

Identify viral sequences from multiple environments

DNA Metagenomic samples from hydrothermal vents, desert halites and hypersaline were used to find viral sequences

Virus identification with Vibrant

We identified two complete viral genomes of hydrothermal vent one of ssDNA and other of dsDNA

We identified some auxiliary metabolic genes (AMGs)

AMGs genes.

Viral taxonony assignmet

Using blastn against a database in combination with Megan we assigned the taxonomy to the assemblies

Viral phylogeny

Viral abundance

Viruses of archaea present in desert samples

Viral presence/absence

Gokusovirus is present in vents

Viral presence/absence

Prochlorococcus and Synechococcus viruses in hydrothermal vent

Both are from marine cyanobacterias, the most important components of the prokaryotic phytoplankton

Network of viral metagenomic data

Relationship among the study sites based on the samples

## 
## Attaching package: 'igraph'

## The following objects are masked from 'package:stats':
## 
##     decompose, spectrum

## The following object is masked from 'package:base':
## 
##     union

## Community sizes
##  1  2  3  4  5  6  7  8  9 10 11 
## 10 16  5  7  7  4  3  2  1  1  1

##            Escherichia virus 121Q                        Peduovirus 
##                                 2                                 5 
##                 Vibrio phage VH7D         Acinetobacter phage Acj61 
##                                 2                                 2 
##                 Cyanophage P-RSM1       Pelagibacter phage HTVC008M 
##                                 2                                 3 
##       Prochlorococcus phage P-HM2      Prochlorococcus phage P-RSM4 
##                                 1                                 1 
##      Prochlorococcus phage P-SSM2      Prochlorococcus phage P-SSM3 
##                                 1                                 2 
##      Prochlorococcus phage P-SSM4      Prochlorococcus phage P-SSM7 
##                                 2                                 2 
##               Shigella phage SfII               Shigella phage SfIV 
##                                 5                                 5 
##     Synechococcus phage ACG-2014d     Synechococcus phage ACG-2014g 
##                                 2                                 2 
##   Synechococcus phage metaG-MbCM1       Synechococcus phage S-IOM18 
##                                 2                                 2 
##     Synechococcus phage S-MbCM100  Synechococcus phage S-RIM8 A.HR1 
##                                 1                                 2 
##        Synechococcus phage S-ShM2        Synechococcus phage S-SKS1 
##                                 2                                 2 
##         Synechococcus phage S-SM1        Synechococcus phage S-SSM7 
##                                 1                                 2 
##       Pelagibacter phage HTVC019P                  Podovirus Lau218 
##                                 1                                 3 
##            Pseudomonas virus F116          Enterobacter phage Enc34 
##                                 4                                 1 
##           Escherichia virus HK630     Enterobacteria phage YYZ-2008 
##                                 5                                 5 
##             Pseudomonas phage F10        Stx2-converting phage 1717 
##                                 1                                 5 
##           Roseobacter virus RDJL1                     Herpesviridae 
##                                 7                                 4 
##                        Inoviridae               Marine gokushovirus 
##                                 4                                 4 
##    Ectocarpus siliculosus virus 1 Aureococcus anophagefferens virus 
##                                 7                                 3 
##             Haloarcula virus His2                  Halovirus HCTV-2 
##                                 6                                 6 
##                  Halovirus HHTV-1                  Halovirus HHTV-2 
##                                 8                                 6 
##        unclassified dsDNA viruses                           Atacama 
##                                 4                                 6 
##                         Atacama.1                           Guaymas 
##                                 8                                 1 
##                            Peru_1                            Guymas 
##                                 7                                 2 
##                             Hvent                          DD093004 
##                                 1                                 9 
##                           Hvent.1                           Hvent.2 
##                                 3                                 4 
##                           Hvent.3                        SRR2080393 
##                                 4                                10 
##                           Hvent.4                        SRR2046236 
##                                 3                                11 
##                           Hvent.5 
##                                 5

## Warning in graphjs(metagen_net, vertex.size = 1): mulitple edge widths not yet
## supported

## Community sizes
##  1  2  3  4  5  6  7  8  9 10 11 
## 10 16  5  7  7  4  3  2  1  1  1

## Warning in graphjs(g): mulitple edge widths not yet supported

General overview of viral metagenomics